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Viruses with RNA Genomes

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...

Size and Structure of Viral Genomes

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

Viral Mutations

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...

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Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

Published on: December 29, 2015

Challenges in RNA virus bioinformatics.

Manja Marz¹, Niko Beerenwinkel², Christian Drosten¹

¹Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, Universitätsklinikum Bonn, Institut für Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, Technische Universität Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Helmholtz Center Munich-German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, Institut für theoretische Chemie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria, Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 München, Germany, University of Leipzig, Faculty of Mathematics and Computer Science, Institute for Computer Science, Augustusplatz 10, 04109 Leipzig, Germany, Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Universität Wien, Althanstraße 14, 1090 Wien, Austria, Department of Computer Science and Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany and The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA.

Bioinformatics (Oxford, England)

|March 5, 2014

Summary

This summary is machine-generated.

Computational virology is an under-resourced field. This review highlights challenges and tools for analyzing RNA viruses, focusing on their unique genomic features and evolutionary dynamics.

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Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses

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Published on: December 29, 2015

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

Virology
Bioinformatics
Computational Biology

Background:

Computational studies on virus structure, function, and evolution are significantly underrepresented in bioinformatics research.
Despite medical and biotechnological importance, few bioinformaticians focus on virology, unlike established fields like genomics or sequencing analysis.

Purpose of the Study:

To raise awareness among bioinformaticians about critical needs and challenges in computational virology.
To provide an overview of existing tools and algorithms for analyzing viral data, particularly RNA viruses.

Main Methods:

Focus on RNA viruses due to their complex genome organization, rapid mutation rates, and low evolutionary conservation.
Review of bioinformatics tools for sequence data handling, RNA structure detection, protein family classification, and evolutionary analysis.

Main Results:

Identified specific challenges in analyzing RNA viruses, including compact genomes and high mutation rates.
Summarized current computational approaches for viral sequence analysis, RNA structure identification, protein classification, and evolutionary studies.

Conclusions:

There is a pressing need for increased bioinformatics research dedicated to virology.
Existing and emerging computational tools can address many challenges in understanding viral biology and evolution.